[gmx-users] Protein-DNA simulation LINKS error

Timofey Tyugashev tyugashev at niboch.nsc.ru
Wed Jul 1 14:08:13 CEST 2015

Thanks for the advice, Justin and Mark.

After rerunning the simulation with guanine in the DNA I've found no 
noticeable problems.
Now I'm looking for another possible sources for mistakes.
1.The input PDB file is formatted using amber conventions, i.e. DG5 and 
DG3 for terminal guanosine  residues, CYX for S--S linked cystine and so 
on. Could it result in any erroneous interpretations by pdb2gmx?
2. I think I correctly created 8-oxoguanine entry in amber force field 
files by copying and modifying existing one for normal guanine, but I 
want to re-check myself just to be sure. Is there anything more in-depth 
available than rather laconic instruction from the GROMACS site? I've 
tried searching through the maillist, but looks like nothing similar 
came up (It's a pity that no forum exist, looking for past answers would 
be far simpler).
3. Could an accidental simultaneous execution of two or three jobs on 
one workstation (scheduling script was set incorrectly once) cause LINKS 

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